BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085023.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,930,689 number of mapped reads = 2,674,072 (91.24%) number of supplementary alignments = 15,479 (0.53%) number of secondary alignments = 0 number of mapped bases = 179,402,658 bp number of sequenced bases = 179,339,692 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,281 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2193 >>>>>>> ACTG content number of A's = 50,268,927 bp (28.03%) number of C's = 34,555,459 bp (19.27%) number of T's = 54,955,542 bp (30.64%) number of G's = 39,552,714 bp (22.05%) number of N's = 7,050 bp (0%) GC percentage = 41.32% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,520,541 number of insertions = 12,797 mapped reads with insertion percentage = 0.47% number of deletions = 36,826 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.399X There is a 4.81% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17579908 0.0705310499507241 0.5610177141744616 chr2 243199373 18010069 0.07405475095529955 0.5354438712006516 chr3 198022430 10877776 0.0549320397694342 0.27462415894006437 chr4 191154276 11468408 0.05999556086310096 0.2927240854268292 chr5 180915260 8829413 0.04880413625694151 0.2563907052249354 chr6 171115067 12497500 0.07303564916349535 0.3827842891549249 chr7 159138663 14603462 0.09176564465669791 0.4714016464997773 chr8 146364022 11265229 0.07696720031374923 0.6314317412885977 chr9 141213431 5876259 0.041612606948130876 0.3828297494257733 chr10 135534747 10498471 0.0774596273824896 0.478316022756139 chr11 135006516 8696187 0.06441309099480798 0.41043185949564065 chr12 133851895 7265520 0.05428029240826213 0.2797278303012633 chr13 115169878 3574059 0.031032932065795885 0.202509002021657 chr14 107349540 5986308 0.05576463578698148 0.30103951208873025 chr15 102531392 2965706 0.028924858447254866 0.20716734975479026 chr16 90354753 4205049 0.046539322618700536 0.26497408045888304 chr17 81195210 3075311 0.03787552246000719 0.2595254005229385 chr18 78077248 4940061 0.0632714539323927 0.641768702839296 chr19 59128983 2587808 0.04376547453894142 0.4114215449957835 chr20 63025520 4039612 0.0640948618908658 0.29949777454384024 chr21 48129895 2347261 0.04876929401154937 0.2730991078504489 chr22 51304566 1196944 0.023330165194263605 0.17389315535098548 chrMT 16571 10869 0.6559048940920886 0.9561285013797378 chrX 155270560 6662069 0.04290619548226013 0.281284219001093 chrY 59373566 343399 0.0057837017907935665 0.11818325236698922